AMBER Archive (2009)

Subject: [AMBER] pmemd running very slow in amber10

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu May 14 2009 - 00:41:40 CDT

Dear amber users,

I have installed amber10 and pmemd in altix4700.
All the installation went well without error after guidance from amber mailing list.

If I run sander.MPI in amber10, it runs fine, but if I run pmemd it run very slow. I run my script not using PBS but directly.

Here I give my *.in file and the *.out file contents.

*in file
=========Dynamic Simulation with Constant Pressure
 &cntrl
   imin=0,
   irest=1, ntx=7,
   iwrap = 1, ntxo=1,
   scnb=1.0, scee=1.0,
   ntt=3, gamma_ln = 1.0,
   tempi = 300.0, temp0=300.0, tautp=0.2,
   ntb = 2, ntp=1, taup=0.2,
   ntf=2,ntc=2,
   nstlim=100000, dt=0.001,
   ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
   ntr=0,
 /

*.out
============

          -------------------------------------------------------
          Amber 10 SANDER 2008
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 10

| Run on 05/14/2009 at 13:32:03

  [-O]verwriting output

File Assignments:
| MDIN: MD-betaMalto-lowLyo.in
| MDOUT: betaMalto-lowLyo-MD00-run0000.out
| INPCRD: e2malto-lowLyo-equi21.rst_100000
| PARM: maltose-lowLyo.top
| RESTRT: betaMalto-lowLyo-MD01-run0100.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: betaMalto-lowLyo-MD00-run0000.traj
| MDINFO: mdinfo
|LOGFILE: logfile

 
 Here is the input file:
 
Dynamic Simulation with Constant Pressure
 &cntrl
   imin=0,
   irest=1, ntx=7,
   iwrap = 1, ntxo=1,
   scnb=1.0, scee=1.0,
   ntt=3, gamma_ln = 1.0,
   tempi = 300.0, temp0=300.0, tautp=0.2,
   ntb = 2, ntp=1, taup=0.2,
   ntf=2,ntc=2,
   nstlim=100000, dt=0.001,
   ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
   ntr=0,
 /
                                                                               

 
 
| Conditional Compilation Defines Used:
| MPI
| SLOW_INDIRECTVEC
| PUBFFT
| MKL
 
| Largest sphere to fit in unit cell has radius = 24.102

| New format PARM file being parsed.
| Version = 1.000 Date = 06/23/08 Time = 17:06:22
| Duplicated 0 dihedrals

| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

 getting new box info from bottom of inpcrd

 NATOM = 23736 NTYPES = 9 NBONH = 14776 MBONA = 9216
 NTHETH = 27648 MTHETA = 12032 NPHIH = 45312 MPHIA = 21248
 NHPARM = 0 NPARM = 0 NNB = 123552 NRES = 1256
 NBONA = 9216 NTHETA = 12032 NPHIA = 21248 NUMBND = 9
 NUMANG = 14 NPTRA = 20 NATYP = 9 NPHB = 1
 IFBOX = 1 NMXRS = 81 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Coordinate Index Table dimensions: 18 9 10
| Direct force subcell size = 5.1696 5.3561 5.0569

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 7, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 100, ntrx = 1, ntwr = -50000
     iwrap = 1, ntwx = 100, ntwv = 0, ntwe = 100
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 2, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
     scnb = 1.00000, scee = 1.00000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Molecular dynamics:
     nstlim = 100000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 20.00000

Langevin dynamics temperature regulation:
     ig = 71277
     temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000

Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 0.20000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1

| Energy averages sample interval:
| ene_avg_sampling = 100

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 93.053 Box Y = 48.205 Box Z = 50.569
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 96 NFFT2 = 50 NFFT3 = 54
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

| PMEMD ewald parallel performance parameters:
| block_fft = 1
| fft_blk_y_divisor = 4
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords = 4012.500 ps

 Number of triangulated 3-point waters found: 1000

     Sum of charges from parm topology file = 0.00000000
     Forcing neutrality...

| Dynamic Memory, Types Used:
| Reals 908174
| Integers 1893246

| Nonbonded Pairs Initial Allocation: 168376

| Running AMBER/MPI version on 64 nodes

 
--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3338E-14 at 2.509280
| CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360
 ---------------------------------------------------

 NSTEP = 100 TIME(PS) = 4012.600 TEMP(K) = 301.34 PRESS = -45.6
 Etot = 72323.5211 EKtot = 16896.3909 EPtot = 55427.1302
 BOND = 4331.7919 ANGLE = 12660.8451 DIHED = 3557.8100
 1-4 NB = 5543.6944 1-4 EEL = 112668.1311 VDWAALS = -10250.7744
 EELEC = -73084.3679 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 1136.7441 VIRIAL = 1359.7065 VOLUME = 226657.6514
                                                    Density = 1.0897
 Ewald error estimate: 0.1325E-03
 ------------------------------------------------------------------------------

 NSTEP = 200 TIME(PS) = 4012.700 TEMP(K) = 300.36 PRESS = 51.9
 Etot = 72308.4304 EKtot = 16841.3962 EPtot = 55467.0342
 BOND = 4223.5093 ANGLE = 12742.0334 DIHED = 3598.7024
 1-4 NB = 5569.0962 1-4 EEL = 112679.4301 VDWAALS = -10228.2235
 EELEC = -73117.5137 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 1124.6180 VIRIAL = 870.8898 VOLUME = 226443.8438
                                                    Density = 1.0907
 Ewald error estimate: 0.8322E-04
 ------------------------------------------------------------------------------

I dont know what is the error.
Can anyone help?

Thank you in advance.

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
 vjramana_at_gmail.com

      

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